Comparative genomic analyses among closely related species can greatly enhance our understanding of plant gene and genome evolution. We report de novo-assembled AA-genome sequences for Oryza nivara, Oryza glaberrima, Oryza barthii, Oryza glumaepatula, and Oryza meridionalis. Our analyses reveal massive levels of genomic structural variation, including segmental duplication and rapid gene family turnover, with particularly high instability in defense-related genes. We show, on a genomic scale, how lineage-specific expansion or contraction of gene families has led to their morphological and reproductive diversification, thus enlightening the evolutionary process of speciation and adaptation. Despite strong purifying selective pressures on most Oryza genes, we documented a large number of positively selected genes, especially those genes involved in flower development, reproduction, and resistance-related processes. These diversifying genes are expected to have played key roles in adaptations to their ecological niches in Asia, South America, Africa and Australia. Extensive variation in noncoding RNA gene numbers, function enrichment, and rates of sequence divergence might also help account for the different genetic adaptations of these rice species. Collectively, these resources provide new opportunities for evolutionary genomics, numerous insights into recent speciation, a valuable database of functional variation for crop improvement, and tools for efficient conservation of wild rice germplasm.
1.Chinese Acad Sci, Kunming Inst Bot, Germplasm Bank Wild Species Southwest China, Plant Germplasm & Genom Ctr, Kunming 650201, Peoples R China 2.Univ Chinese Acad Sci, Beijing 100039, Peoples R China 3.Kunming Univ Sci & Technol, Fac Life Sci & Technol, Kunming 650500, Peoples R China 4.Yunnan Acad Agr Sci, Inst Cereal Crop Sci, Kunming 650205, Peoples R China 5.Northeastern State Univ, Dept Nat Sci, Broken Arrow, OK 74014 USA 6.Univ Georgia, Dept Genet, Athens, GA 30602 USA
Zhang,Qun-Jie;Zhu,Ting;Xia,En-Hua;Shi,Chao;Liu,Yun-Long;Zhang,Yun;Liu,Yuan;Jiang,Wen-Kai;Zhao,You-Jie;Mao,Shu-Yan;Zhang,Li-Ping;Huang,Hui;Jiao,Jun-Ying;Xu,Ping-Zhen;Yao,Qiu-Yang;Zeng,Fan-Chun;Yang,Li-Li;Gao,Ju;Tao,Da-Yun;Wang,Yue-Ju;Bennetzen,Jeffrey L.;Gao,Li-Zhi.Rapid diversification of five Oryza AA genomes associated with rice adaptation,PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA,2014,70(44):8236-8243